Starting phenix.real_space_refine on Wed Jul 1 21:29:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypq_34011/07_2026/7ypq_34011.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.137 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 12 5.16 5 C 1811 2.51 5 N 493 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2915 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 0.91, per 1000 atoms: 0.31 Number of scatterers: 2915 At special positions: 0 Unit cell: (65.55, 79.8, 75.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 11 15.00 O 588 8.00 N 493 7.00 C 1811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 98.3 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 634 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 18.7% alpha, 48.6% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.742A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 336 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 66 removed outlier: 6.671A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N LEU A 112 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A 84 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE A 114 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 86 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 116 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 108 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 114 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN A 106 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 116 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.221A pdb=" N LEU A 236 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU A 184 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 238 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 186 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 240 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N SER A 239 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N CYS A 226 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 217 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 14.863A pdb=" N LEU A 146 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 13.885A pdb=" N GLU A 172 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 148 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU A 170 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N PHE A 150 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 168 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 152 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 4.579A pdb=" N VAL A 348 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 347 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 369 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 349 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 367 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 351 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 102 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 919 1.34 - 1.46: 637 1.46 - 1.57: 1394 1.57 - 1.69: 21 1.69 - 1.81: 19 Bond restraints: 2990 Sorted by residual: bond pdb=" C3' DA Q 4 " pdb=" O3' DA Q 4 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" C3' DA Q 5 " pdb=" O3' DA Q 5 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" C LEU A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.330 1.302 0.028 1.26e-02 6.30e+03 4.94e+00 bond pdb=" C3' DA Q 1 " pdb=" C2' DA Q 1 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.48e+00 bond pdb=" O4' DA Q 5 " pdb=" C1' DA Q 5 " ideal model delta sigma weight residual 1.420 1.397 0.023 1.10e-02 8.26e+03 4.46e+00 ... (remaining 2985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 3869 1.32 - 2.65: 179 2.65 - 3.97: 26 3.97 - 5.29: 5 5.29 - 6.62: 2 Bond angle restraints: 4081 Sorted by residual: angle pdb=" O4' DA Q 1 " pdb=" C4' DA Q 1 " pdb=" C3' DA Q 1 " ideal model delta sigma weight residual 106.00 104.48 1.52 6.00e-01 2.78e+00 6.44e+00 angle pdb=" O4' DA Q 2 " pdb=" C4' DA Q 2 " pdb=" C3' DA Q 2 " ideal model delta sigma weight residual 106.00 104.50 1.50 6.00e-01 2.78e+00 6.26e+00 angle pdb=" CA GLU A 216 " pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " ideal model delta sigma weight residual 114.10 119.08 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" O5' DA Q 5 " pdb=" C5' DA Q 5 " pdb=" C4' DA Q 5 " ideal model delta sigma weight residual 109.40 111.37 -1.97 8.00e-01 1.56e+00 6.07e+00 angle pdb=" O4' DA Q 7 " pdb=" C4' DA Q 7 " pdb=" C3' DA Q 7 " ideal model delta sigma weight residual 106.00 107.36 -1.36 6.00e-01 2.78e+00 5.11e+00 ... (remaining 4076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1553 17.98 - 35.96: 180 35.96 - 53.94: 56 53.94 - 71.92: 12 71.92 - 89.90: 4 Dihedral angle restraints: 1805 sinusoidal: 823 harmonic: 982 Sorted by residual: dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N LEU A 352 " pdb=" CA LEU A 352 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 219 " pdb=" C PHE A 219 " pdb=" N ASN A 220 " pdb=" CA ASN A 220 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N LYS A 305 " pdb=" CA LYS A 305 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 267 0.035 - 0.070: 130 0.070 - 0.104: 38 0.104 - 0.139: 22 0.139 - 0.174: 2 Chirality restraints: 459 Sorted by residual: chirality pdb=" C3' DA Q 5 " pdb=" C4' DA Q 5 " pdb=" O3' DA Q 5 " pdb=" C2' DA Q 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA ILE A 310 " pdb=" N ILE A 310 " pdb=" C ILE A 310 " pdb=" CB ILE A 310 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 456 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 377 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 378 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 216 " 0.004 2.00e-02 2.50e+03 7.45e-03 5.55e-01 pdb=" C GLU A 216 " -0.013 2.00e-02 2.50e+03 pdb=" O GLU A 216 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS A 217 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.004 2.00e-02 2.50e+03 7.39e-03 5.46e-01 pdb=" C ILE A 297 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 298 " 0.004 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 611 2.79 - 3.32: 2563 3.32 - 3.84: 4682 3.84 - 4.37: 5819 4.37 - 4.90: 9706 Nonbonded interactions: 23381 Sorted by model distance: nonbonded pdb=" O CYS A 210 " pdb=" OG SER A 214 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 98 " pdb=" NE2 GLN A 243 " model vdw 2.360 3.120 nonbonded pdb=" OG SER A 292 " pdb=" OP1 DA Q 9 " model vdw 2.402 3.040 nonbonded pdb=" NH2 ARG A 223 " pdb=" O ASN A 241 " model vdw 2.413 3.120 nonbonded pdb=" O ASN A 358 " pdb=" OD1 ASN A 358 " model vdw 2.421 3.040 ... (remaining 23376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.440 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2990 Z= 0.300 Angle : 0.650 6.618 4081 Z= 0.403 Chirality : 0.048 0.174 459 Planarity : 0.002 0.029 481 Dihedral : 17.794 89.903 1171 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.46), residues: 323 helix: 0.04 (0.66), residues: 62 sheet: -0.22 (0.45), residues: 125 loop : -0.73 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 294 TYR 0.010 0.001 TYR A 299 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.30 ( 2990) covalent geometry : angle 0.65050 / 0.40 ( 4081) hydrogen bonds : bond 0.12357 / 6.63 ( 102) hydrogen bonds : angle 7.17021 / 4.77 ( 291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.104 Fit side-chains REVERT: A 80 ASN cc_start: 0.8098 (m110) cc_final: 0.7333 (t0) REVERT: A 130 CYS cc_start: 0.8140 (m) cc_final: 0.7935 (m) REVERT: A 206 ASP cc_start: 0.7749 (m-30) cc_final: 0.7522 (m-30) REVERT: A 262 TYR cc_start: 0.8966 (p90) cc_final: 0.8652 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0686 time to fit residues: 4.5514 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.167633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.121189 restraints weight = 2970.960| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.13 r_work: 0.3115 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2990 Z= 0.194 Angle : 0.606 8.042 4081 Z= 0.336 Chirality : 0.045 0.136 459 Planarity : 0.003 0.023 481 Dihedral : 16.871 71.170 510 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.97 % Allowed : 3.87 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.46), residues: 323 helix: 0.62 (0.68), residues: 62 sheet: -0.12 (0.45), residues: 125 loop : -0.70 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.010 0.001 TYR A 351 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 2990) covalent geometry : angle 0.60576 / 0.34 ( 4081) hydrogen bonds : bond 0.03964 / 2.28 ( 102) hydrogen bonds : angle 5.89059 / 3.93 ( 291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8270 (m110) cc_final: 0.7441 (t0) REVERT: A 130 CYS cc_start: 0.8410 (m) cc_final: 0.8043 (m) REVERT: A 213 LYS cc_start: 0.8487 (mttm) cc_final: 0.8021 (mptt) REVERT: A 262 TYR cc_start: 0.9021 (p90) cc_final: 0.8634 (p90) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.0709 time to fit residues: 3.9548 Evaluate side-chains 44 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.167194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120333 restraints weight = 2976.692| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.15 r_work: 0.3091 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2990 Z= 0.194 Angle : 0.575 6.164 4081 Z= 0.324 Chirality : 0.045 0.142 459 Planarity : 0.003 0.023 481 Dihedral : 16.960 73.122 510 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 6.45 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.47), residues: 323 helix: 0.89 (0.70), residues: 62 sheet: 0.04 (0.46), residues: 122 loop : -0.54 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.013 0.002 TYR A 260 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 2990) covalent geometry : angle 0.57523 / 0.32 ( 4081) hydrogen bonds : bond 0.03721 / 2.16 ( 102) hydrogen bonds : angle 5.52887 / 3.68 ( 291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8174 (m110) cc_final: 0.7365 (t0) REVERT: A 130 CYS cc_start: 0.8381 (m) cc_final: 0.8026 (m) REVERT: A 262 TYR cc_start: 0.9029 (p90) cc_final: 0.8644 (p90) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.0671 time to fit residues: 3.7757 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122263 restraints weight = 2943.200| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.20 r_work: 0.3119 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2990 Z= 0.139 Angle : 0.533 5.922 4081 Z= 0.302 Chirality : 0.043 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.233 74.841 510 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.29 % Allowed : 9.35 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.47), residues: 323 helix: 1.18 (0.70), residues: 62 sheet: 0.08 (0.46), residues: 120 loop : -0.52 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.008 0.001 TYR A 218 PHE 0.009 0.001 PHE A 258 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 2990) covalent geometry : angle 0.53333 / 0.30 ( 4081) hydrogen bonds : bond 0.03220 / 1.92 ( 102) hydrogen bonds : angle 5.24622 / 3.51 ( 291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8271 (m110) cc_final: 0.7438 (t0) REVERT: A 130 CYS cc_start: 0.8332 (m) cc_final: 0.8002 (m) REVERT: A 213 LYS cc_start: 0.8428 (mttm) cc_final: 0.7908 (mptt) REVERT: A 262 TYR cc_start: 0.9012 (p90) cc_final: 0.8730 (p90) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.0536 time to fit residues: 3.2369 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.168842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121215 restraints weight = 2903.339| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.20 r_work: 0.3118 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2990 Z= 0.170 Angle : 0.535 5.183 4081 Z= 0.301 Chirality : 0.043 0.139 459 Planarity : 0.002 0.021 481 Dihedral : 17.706 75.106 510 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 9.35 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.47), residues: 323 helix: 1.25 (0.71), residues: 62 sheet: 0.11 (0.46), residues: 120 loop : -0.54 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.020 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 2990) covalent geometry : angle 0.53518 / 0.30 ( 4081) hydrogen bonds : bond 0.03217 / 1.93 ( 102) hydrogen bonds : angle 5.17039 / 3.46 ( 291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8159 (m110) cc_final: 0.7326 (t0) REVERT: A 130 CYS cc_start: 0.8373 (m) cc_final: 0.8037 (m) REVERT: A 213 LYS cc_start: 0.8446 (mttm) cc_final: 0.7930 (mptt) REVERT: A 262 TYR cc_start: 0.9020 (p90) cc_final: 0.8595 (p90) outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 0.0554 time to fit residues: 3.0862 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121738 restraints weight = 2909.186| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.21 r_work: 0.3115 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2990 Z= 0.151 Angle : 0.515 4.716 4081 Z= 0.291 Chirality : 0.043 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.693 76.272 510 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.94 % Allowed : 9.68 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.47), residues: 323 helix: 1.30 (0.71), residues: 62 sheet: 0.13 (0.46), residues: 120 loop : -0.55 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.013 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 2990) covalent geometry : angle 0.51482 / 0.29 ( 4081) hydrogen bonds : bond 0.03115 / 1.87 ( 102) hydrogen bonds : angle 5.09459 / 3.41 ( 291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8163 (m110) cc_final: 0.7344 (t0) REVERT: A 130 CYS cc_start: 0.8356 (m) cc_final: 0.8029 (m) REVERT: A 213 LYS cc_start: 0.8451 (mttm) cc_final: 0.7944 (mptt) REVERT: A 262 TYR cc_start: 0.9024 (p90) cc_final: 0.8596 (p90) REVERT: A 305 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8377 (mmmt) outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.0446 time to fit residues: 2.7044 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.169190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121368 restraints weight = 2962.710| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.24 r_work: 0.3105 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2990 Z= 0.161 Angle : 0.520 4.725 4081 Z= 0.295 Chirality : 0.043 0.138 459 Planarity : 0.002 0.020 481 Dihedral : 17.685 77.043 510 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.94 % Allowed : 10.32 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.47), residues: 323 helix: 1.31 (0.71), residues: 62 sheet: 0.17 (0.46), residues: 120 loop : -0.54 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.012 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 2990) covalent geometry : angle 0.52043 / 0.29 ( 4081) hydrogen bonds : bond 0.03083 / 1.85 ( 102) hydrogen bonds : angle 5.04977 / 3.39 ( 291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8181 (m110) cc_final: 0.7341 (t0) REVERT: A 130 CYS cc_start: 0.8368 (m) cc_final: 0.8027 (m) REVERT: A 213 LYS cc_start: 0.8455 (mttm) cc_final: 0.7942 (mptt) REVERT: A 262 TYR cc_start: 0.9027 (p90) cc_final: 0.8597 (p90) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.0456 time to fit residues: 2.6696 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.167732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120981 restraints weight = 2981.102| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.19 r_work: 0.3102 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2990 Z= 0.176 Angle : 0.531 4.529 4081 Z= 0.299 Chirality : 0.043 0.139 459 Planarity : 0.002 0.020 481 Dihedral : 17.681 78.142 510 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 10.97 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.47), residues: 323 helix: 1.27 (0.71), residues: 62 sheet: 0.15 (0.46), residues: 120 loop : -0.56 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.012 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 2990) covalent geometry : angle 0.53106 / 0.30 ( 4081) hydrogen bonds : bond 0.03135 / 1.89 ( 102) hydrogen bonds : angle 5.04351 / 3.39 ( 291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8175 (m110) cc_final: 0.7338 (t0) REVERT: A 130 CYS cc_start: 0.8365 (m) cc_final: 0.8023 (m) REVERT: A 213 LYS cc_start: 0.8493 (mttm) cc_final: 0.7996 (mptt) REVERT: A 262 TYR cc_start: 0.9027 (p90) cc_final: 0.8602 (p90) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.0416 time to fit residues: 2.4495 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.168210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120769 restraints weight = 2992.611| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.22 r_work: 0.3098 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2990 Z= 0.172 Angle : 0.546 7.305 4081 Z= 0.303 Chirality : 0.043 0.138 459 Planarity : 0.002 0.019 481 Dihedral : 17.676 79.056 510 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 10.97 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.47), residues: 323 helix: 1.27 (0.71), residues: 62 sheet: 0.14 (0.46), residues: 120 loop : -0.55 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 2990) covalent geometry : angle 0.54611 / 0.30 ( 4081) hydrogen bonds : bond 0.03107 / 1.87 ( 102) hydrogen bonds : angle 5.02761 / 3.38 ( 291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.061 Fit side-chains REVERT: A 80 ASN cc_start: 0.8190 (m110) cc_final: 0.7343 (t0) REVERT: A 99 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6361 (mmmt) REVERT: A 113 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 130 CYS cc_start: 0.8367 (m) cc_final: 0.8015 (m) REVERT: A 213 LYS cc_start: 0.8482 (mttm) cc_final: 0.7979 (mptt) REVERT: A 262 TYR cc_start: 0.9026 (p90) cc_final: 0.8600 (p90) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0400 time to fit residues: 2.2828 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.168306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120905 restraints weight = 2963.645| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.22 r_work: 0.3107 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2990 Z= 0.167 Angle : 0.543 7.483 4081 Z= 0.302 Chirality : 0.043 0.138 459 Planarity : 0.002 0.022 481 Dihedral : 17.675 79.404 510 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 11.94 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.47), residues: 323 helix: 1.27 (0.71), residues: 62 sheet: 0.14 (0.46), residues: 120 loop : -0.56 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 2990) covalent geometry : angle 0.54260 / 0.30 ( 4081) hydrogen bonds : bond 0.03082 / 1.85 ( 102) hydrogen bonds : angle 5.01952 / 3.37 ( 291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.114 Fit side-chains REVERT: A 80 ASN cc_start: 0.8186 (m110) cc_final: 0.7342 (t0) REVERT: A 99 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6350 (mmmt) REVERT: A 113 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 130 CYS cc_start: 0.8367 (m) cc_final: 0.8019 (m) REVERT: A 213 LYS cc_start: 0.8475 (mttm) cc_final: 0.7979 (mptt) REVERT: A 262 TYR cc_start: 0.9026 (p90) cc_final: 0.8599 (p90) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0473 time to fit residues: 2.7143 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.166785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120154 restraints weight = 2966.129| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.18 r_work: 0.3099 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2990 Z= 0.198 Angle : 0.569 7.354 4081 Z= 0.314 Chirality : 0.044 0.142 459 Planarity : 0.002 0.020 481 Dihedral : 17.690 80.258 510 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 13.23 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.47), residues: 323 helix: 1.21 (0.70), residues: 62 sheet: 0.15 (0.46), residues: 120 loop : -0.58 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 2990) covalent geometry : angle 0.56889 / 0.31 ( 4081) hydrogen bonds : bond 0.03173 / 1.91 ( 102) hydrogen bonds : angle 5.03966 / 3.39 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 765.35 seconds wall clock time: 13 minutes 49.05 seconds (829.05 seconds total)